Biological data annotation and visualization

ABSTRACT

Dynamic linking of pathway maps and cell maps is disclosed in certain embodiments. In such embodiments, the pathway maps are linked to spatially-localized regional nucleic acid data (e.g., sequence data), as opposed to non-spatially selected nucleic acid data. The pathway map and cell map data may be linked so that interactions results in changes or updates to the linked map, such as the selection or highlighting of cells exhibiting pathway map characteristics specified by a user of updating of node values or states to correspond to that of a cell or cells selected by the user.

BACKGROUND

The subject matter disclosed herein relates to the association andanalysis of biological and biochemical data acquired from a variety ofsources.

The proliferation of biological and biochemical tools has led tosubstantial increases in the amount of information available aboutbiological and biochemical systems, though it may be difficult toassociate the myriad types and sources of information together in ameaningful manner. As a result, information may be available that isdifficult to parse in isolation but which is also difficult to easilyassociate with related information that would yield insight whenanalyzed in combination.

It is now possible to acquire expression data for both proteins andnucleic acid sequences for both patients and populations, as well assequence data for both proteins and nucleic acid sites. In addition,cellular level data and images can be acquired. However, each of thesedifferent types of information are typically acquired using differenttypes of processes and/or systems, and thus may not be readilycombinable or associated. Thus, despite the extent of this informationthat can be obtained and existing knowledge of the associated regulatorypathways, it may still be difficult to fully exploit the extent of theinformation that may be available.

By way of example, even with a full array of conventional dataacquisition and analysis tool, deciphering deregulated pathways andbiological states in complex diseases in an individual or a populationmay remain challenging. For instance, there are over 20,000protein-encoding genes in the human genome. Most signaling and metabolicpathways involve 100's if not 1,000's of essential genes, RNA andprotein molecules in specific molecular states (e.g. phosphorylation,binding) and cellular compartments (nucleus, cytosol, plasma membrane).The large number of molecule types, their concentrations in differentcells and sub-cellular compartments, and the dynamics of biologicalprocesses are just some of the challenges faced in associating andanalyzing available biological and biochemical data.

BRIEF DESCRIPTION

In one embodiment, a computer-based method is provided for interactivelyevaluating image and data for a tissue sample. In accordance with thismethod, a pathway map is displayed comprising a plurality of nodeslinked to nucleic acid sequence data for one or more spatially localizedregions-of-interest within a tissue sample. A cell map is displayeddepicting a set of cells present within a field-of-view of the tissuesample. The cell map is linked to a plurality of biomarker expressiondata displayed for the tissue sample. One or more inputs are receivedspecifying values or states for one or more nodes of the pathway map.Based on the one or more inputs, cells within the cell map that exhibitbiomarker expression corresponding to the values or states specified forthe one or more nodes are highlighted.

In a further embodiment, a computer-based method is provided forinteractively evaluating image and data for a tissue sample. Inaccordance with this method, a pathway map is displayed comprising aplurality of nodes linked to nucleic acid sequence data for one or morespatially localized regions-of-interest within a tissue sample. A cellmap is displayed depicting a set of cells present within a field-of-viewof the tissue sample. The cell map is linked to a plurality of biomarkerexpression data for the tissue sample. One or more inputs are receivedselecting one or more cells of the cell map. Based on the one or moreinputs, values or states of one or more nodes within the pathway map areset to correspond to the nucleic acid characteristics of the one or moreselected cells.

In an additional embodiment, a processor-based system is provided. Theprocessor-based system includes one or both of a memory or storagedevice storing one or more executable routines for the analysis ofregion-specific nucleic acid sequence data and cellular or sub-cellularbiomarker expression data and one or more processors configured toexecute the one or more executable routines. The one or more routines,when executed, cause acts to be performed comprising: displaying apathway map comprising a plurality of nodes linked to nucleic acidsequence data for one or more spatially localized regions-of-interestwithin a tissue sample; displaying a cell map depicting a set of cellspresent within a field-of-view of the tissue sample, wherein the cellmap is linked to a plurality of biomarker expression data for the tissuesample; receiving inputs setting one or more node values or stateswithin the pathway map or selecting one or more cells within the cellmap; if the inputs set one or more node values or states within thepathway map, highlighting cells within the cell map that exhibitbiomarker expression corresponding to the values or states specified forthe one or more nodes; or if the inputs select one or more cells withinthe cell map, setting values of one or more nodes within the pathway mapto correspond to the nucleic acid characteristics of the one or moreselected cells.

BRIEF DESCRIPTION OF THE DRAWINGS

These and other features, aspects, and advantages of the presentinvention will become better understood when the following detaileddescription is read with reference to the accompanying drawings in whichlike characters represent like parts throughout the drawings, wherein:

FIG. 1 is a block diagram of an embodiment of a processor-based systemfor integrating, displaying, and querying data, in accordance withaspects of the present disclosure;

FIG. 2 is a high-level depiction of the aggregation of different datasources and types for use in a query tool, in accordance with aspects ofthe present disclosure;

FIG. 3 depicts a tissue sample suitable for imaging and acquiringcellular samples, in accordance with aspects of the present disclosure;

FIG. 4 shows a sample screen depicting associated cell image and pathwaymap data, in accordance with aspects of the present disclosure;

FIG. 5 depicts an example of visual annotation that may be associatedwith a pathway node to convey subject specific measurement data, inaccordance with aspects of the present disclosure;

FIG. 6 shows a sample screen depicting associated cell image and pathwaymap data, in accordance with further aspects of the present disclosure;

FIG. 7 shows a sample screen depicting associated cell image and pathwaymap data, in accordance with additional aspects of the presentdisclosure;

FIG. 8 shows a sample screen depicting associated cell image and pathwaymap data, in accordance with further aspects of the present disclosure;

FIG. 9A and 9B collectively show a sample screen depicting associatedcell image and pathway map data in conjunction with a calculated slideview and select regions of interest, in accordance with further aspectsof the present disclosure;

FIG. 10 shows a sample screen depicting associated cell image andpathway map data, in accordance with further aspects of the presentdisclosure;

FIG. 11 shows a sample screen depicting annotated pathway map data andtabular analysis results, in accordance with aspects of the presentdisclosure;

FIG. 12 shows a sample screen depicting pathway map data and tabularanalysis results, in accordance with further aspects of the presentdisclosure;

FIG. 13 depicts a statistical analysis for a GWAS analysis, inaccordance with further aspects of the present disclosure;

FIG. 14 depicts a process flow diagram for a GSEA analysis, inaccordance with further aspects of the present disclosure;

FIG. 15 depicts a process flow illustrating identification of regions ofinterest using the present approaches, in accordance with furtheraspects of the present disclosure; and

FIG. 16 depicts a process flow illustrating acquisition of DNA sequencedata in a homogeneous context using the present approaches, inaccordance with further aspects of the present disclosure.

DETAILED DESCRIPTION

The present discussion relates to associating and analyzing biologicaland biochemical data (including expression, sequence, and image data)from disparate sources to facilitate analysis and understanding. By wayof example, certain approaches discussed herein may be useful ininterpreting multiplexed immunofluorescence (IF) and fluorescent in situhybridization (FISH) tissue image measurements in a context of pathwaysand biological processes. Such analyses may have previously beenchallenging given the limited number of probe measures relative to thelarge number of pathways and system network states. Integration of IFand FISH tissue measures with other types of data (including, but notlimited to: genomics, transcriptomics, proteomics, and metabolomics, andso forth) has also been difficult using conventional approaches. Yetincreasingly such combined or associated measures from a subject may bedesirable when trying to decipher deregulated pathways and biologicalstates in complex diseases. With this in mind, the present approachprovides useful tools (e.g., software tools) that facilitate dataintegration, analysis, and visualization in a pathway context.

To provide some context for certain of the data acquisition approachesdiscussed herein and for the amount and type of data involved, Multiomyxtechnology (available from General Electric Company) provides thecapability to measure IF protein concentrations for up to 60 proteinswithin the same cell. Fluorescent in situ hybridization (FISH) probesprovide measurements of RNA and DNA molecules at the cellular level.Having protein and RNA measurements on a per cell basis using suchtechniques is an improvement over traditional grind-and-find approaches,such as flow cytometry, where data at the cellular level may be lost.Instead, the traditional approach is to obtain measures of each proteinand RNA concentration, and DNA sequence averaged over a large number(e.g., millions) of cells. This capability, as discussed herein, toresolve measures of protein, DNA, and RNA expression and/or sequence atthe single cell level while also preserving spatial information providesfor powerful pathway analysis approaches.

In one example, multiplexed IF tissue imaging measures are integratedwith other types of data including, but not limited to, DNA sequencing,RNA expression, and DNA-FISH measures. In one such embodiment, thesedifferent types of data can be overlaid onto (or otherwise integratedinto) biochemical pathway maps and the associated data used to performone or both of gene set enrichment analysis and pathway scoringanalysis. From within the combined data, features may be interactivelyselected and/or manipulated from among the high content data, withresulting impacts or selections shown in the pathway views. Furthermore,in certain implementations, a researcher can select a specific pathwaystate and then query cells that exhibit the selected state to view howthe cells are spatially distributed in the tissue.

The present discussion, therefore, provides for the use of tools in theanalysis, modeling, simulation, and/or representation of biological datadrawn from disparate sources. As discussed herein, the present tools maybe embodied and implemented as executable applications running on aprogrammed general-purpose or application-specific processor-basedplatform. Prior to describing in detail the operation of suchapplications, an example of a suitable processor-based system 10 isbriefly discussed with reference to FIG. 1. In particular, FIG. 1 is ablock diagram of an embodiment of a processor-based system 10 forintegrating, annotating, visualizing, and querying biological and/orbiochemical data drawn from various sources, as discussed herein.

Input data 12 may be directly input by one or more users, may beacquired from an imaging or sequencing system at a local or remotelocation, may be acquired from a database of patient records, researcheror physician notes, clinical studies, or online research tools, or maybe acquired from other local or network accessible resources. The inputdata 12 may be provided to the processing device 14 in a variety ofstandard and/or non-standard data formats (e.g., image files, binaryfiles, text files, spreadsheets, databases, etc.), and the data mayinclude varying levels of detail, common or differing nomenclature,and/or common or different color, coordinate, or reference systems. Theinput data 12, as discussed herein, is provided to a processing device14, which is used to execute one or more operations on the input data 12in accordance with present embodiments, such as to integrate, visualize,and/or query the data 12 in a raw or processed form.

The processing device 14 includes one or more processors 18, memorydevices 20, and storage devices 22. The processor(s) 18 may be used toexecute routines as discussed herein for processing the data 12.Moreover, the processor(s) 18 may include one or more microprocessors,such as one or more “general-purpose” microprocessors, one or morespecial-purpose microprocessors and/or application specific integratedcircuits (ASICS).

The memory device(s) 20 may include a volatile memory, such as randomaccess memory (RAM), and/or a nonvolatile memory, such as read-onlymemory (ROM). The memory device(s) 20 may store a variety of informationand may be used for various purposes. For example, the memory device(s)20 may store processor-executable instructions (e.g., firmware orsoftware) for the processor(s) 18 to execute, such as instructions forimplementing the present approaches.

The storage device(s) 22 (e.g., nonvolatile storage) may include ROM,flash memory, a hard drive, or any other suitable optical, magnetic, orsolid-state storage media. The storage device(s) 22 may store data(e.g., input data 12, processing results, etc.), instructions (e.g.,software or firmware for processing data 12, etc.), and so forth.

The depicted processing device 14 includes a user interface 24. The userinterface 24 enables an operator to input parameters associated with theinput data 12 or with the processing of the data 12. The user interface24 also enables an operator to select options or to configure processingof the data 12. As may be appreciated, the user interface 24 may includea keyboard, a mouse, or any suitable device for inputting data, makingselections, and/or operating the processing device 14. Furthermore, theuser interface 24 may include a display to present data, such as thesimulation results data 16. The user interface 24 may also include aprinter for printing data, such as for printing simulation results data16.

With the preceding hardware discussion in mind, approaches discussedherein provide for the design and use of tools to integrate, analyze,and view high content tissue data in a pathway context and/or in atissue view. For example, in certain embodiments, such a tool mayintegrate immunofluorescence (IF) (including multiplexed IF and/or otherbiomarker expression data) and fluorescent in situ hybridization (FISH)tissue imaging measures with other types of data including, but notlimited to, microarray, DNA sequencing and expression measures, and RNAsequencing and expression measures. In certain implementations, such atool may overlay or integrate different types of such data onto pathwayor regulatory maps. In such approaches, the tool may be used to performone or both of gene set enrichment analysis or pathway scoring analysis.Further, the tools, as discussed herein, may be used to interactivelyselect features from the high content data and to show how the selectedfeatures, or changes to these features, impact the pathway view. Inaddition, in certain embodiments a researcher can use such a tool toselect a specific pathway state and to query cells that exhibit thestate for additional details regarding these cells and/or to view howthe cells that exhibit the selected state are spatially distributed inthe tissue. By way of example, IF, FISH, DNA sequence, and/or RNAsequence data may be obtained for or integrated with tissue images,including for different selected regions of interest of the tissueimages. From such views, a user may view variants, copy number, RNA andprotein measures, and so forth (such as for selected regions of intereston the tissue images) on associated pathway maps. Conversely, on theassociated pathway map, selected pathway states or conditions may beidentified and corresponding regions highlighted or shown on the tissueimages, such as down to the cellular or subcellular level. In thismanner, a user may be able to interactively differentiate betweentissues or cells and within tissue samples across multiple pathway mapnodes.

With these concepts in mind, and turning to FIG. 2, a high-level view ofthe relationship between various data sources and the present tool isprovided. In this example, various pipelines 60 corresponding todifferent data sources and types (e.g., DNA sequencing, imaging (IF andFISH), pathway, biomarker expression, and so forth) are shown. Certainof the pipelines 60 (e.g., IF, FISH, and nucleic acid sequencing)originate in wet lab settings 62 (i.e., as the result of clinical ormedical lab work for a patient or cohort of patients). Conversely, otherpipelines may originate from online research community or data storesources, from records of clinical studies, from databases or catalogs ofbiomarker activity and/or pathway maps, and so forth. Patient, clinicaland study data may include demographic data (e.g., gender, age, height,weight, and so forth) as well as other clinical values, such asdiagnoses, symptoms, and so forth. The various pipelines 60 in theseexamples may access data of various types and formats, such as flatfiles or data stored in databases (e.g., relational databases).

With respect to the various types of wet lab data, it is worth notingthat there may not be strict correspondence between the shape and/orsize of sample regions for different techniques. For example, turningbriefly to FIG. 3, an example of a slide 90 on which a tissue sample 92is affixed is shown. Such a slide 90 and tissue sample 92 may besuitable for generating multiplexed IF images, such as a series ofimages, each stained with one or more different IF biomarker probes suchthat each image depicts biomarker expression levels for the respectivebiomarker(s) selected for that round of imaging. When viewing suchimages, a user may specify several respective fields-of-view 94corresponding to a representative portion (e.g., spatial distribution)of the sample 92 and the desired objective strength for the microscopein question.

In addition, one or more sequencing sections or regions 96 may also betaken from the sample 92. For example, such sequencing regions 96 may beextracted or lifted after multiplexed IF imaging and one or both of DNAor RNA sequence and expression levels determined within the region 96.In this manner, sequencing data may be obtained for different spatiallylocalized sections of the sample 92 so that some degree of spatialinformation is retained with respect to the sequence data. As with thefields-of-view 94, the sequencing regions 96 may be selected to berepresentative of and spatially distributed with respect to the sample92.

Though not necessarily to scale, as depicted in FIG. 3, the sequencingregions 96 and the imaging fields-of-view 94 may differ in both size,spatial location, and/or shape, with the depicted example showing thesequencing regions being larger and differently shaped than thefields-of-view 94. In the depicted example, the fields-of-view 94 aresquare and are approximately 0.76 mm across, while the sequencingregions circular and are approximately 2 mm in diameter. As a result, tothe extent that the size, spatial location, and/or shape of thesequencing regions 96 and fields-of-view 94 differ, there may not beprecise correspondence between the sequence or other nucleic acidinformation acquired for a given sequencing region 96 with the biomarkerexpression data acquired for a generally corresponding field-of-view 94.Further, while biomarker expression and other measures generated for agiven field-of-view 94 may be granular to the cellular or sub-cellularlevel, nucleic acid data (sequence and otherwise) acquired for a givensequencing region 96 may be granular only down to the level of thesequencing region. That is, data acquired for a sequencing region 96 maybe aggregated or averaged over the respective sequencing region 96, butnot to a higher level of granularity (e.g., to cells or sub-cellularstructures within the sequencing region 96).

However, as will be appreciated, both the size and shape of thefields-of-view and the sequencing regions 96 will be a function of therespective imaging and sampling technologies employed. Thus, in otherimplementations the sequencing regions 96 may be the same size orsmaller than the fields-of-view 94, including down to the cellular, oreven sub-cellular level to the extent that the sampling technology andsequencing technology permits. Similarly, in other implementations thesequencing regions 96 may be shaped differently than what is shown,including having geometries similar to or the same as the fields-of-view94, or even having arbitrary shapes or distributions, such as where auser specifies the individual cells or groups of cells to be sampled forsequencing.

With this in mind, and turning back to FIG. 2, in the depicted example,the various pipelines 60 may be embodied as or incorporated intorespective submodels 64. Each pipeline 60 may also have an associatedimporter 66 by which the submodel 64 and/or raw or processed dataobtained by the respective pipeline 60 may be imported into anintegrated model 68 and, ultimately, into a database 70 (e.g., an“omics” database). In the depicted example, a harmonization layer 72 mayalso be provided. Such a harmonization layer 72, when present, mayharmonize the respective submodels 64 or datasets to account fordifferences in nomenclature and/or coordinate systems (in the case ofimage data). In addition, in the depicted example an external set ofimage data 74 or image database may be provided that can be referencedby or incorporated into the database 70, such as via one or morereference links.

Lastly, a query layer 80 is provided by which a user may access andinteract with the database 70. By way of example, via the query layer80, a user may formulate a complex biological query based on a questionof interest. The query may in turn be processed by the query layer 80and used to access the relevant data and/or models within the database70. Results of the query may then be analyzed, visualized, and/orexported via the query layer 80.

With the preceding discussion in mind, examples of tool implementationsand uses are provided to facilitate explanation of the present concepts.For example, turning to FIG. 4, a screen 100 is displayed of animplementation of a tool in accordance with the present approach wherethe screen 100 provides a linked, concurrent view of cell map (e.g.,tissue image) and pathway data. In certain implementations theunderlying subject, (e.g., patient) tissue, and/or study data may beselected via a displayed interface 114 (e.g., a study data panel), whereavailable subject, tissue, and/or study data may be displayed, such asin a tree format or a hierarchical list.

In the depicted example, a single pathway map 102 (e.g., a metabolicand/or signaling pathway) and a single cell map 104 are shown, though itshould be appreciated that, depending on the analysis and queries ofinterest, more than one pathway map 102 and/or cell map 104 may bedisplayed at one time, such as in separate panes of the screen 100. Asdiscussed herein, the cell map or tissue images 104 may correspond to animage of a field-of-view 94 taken from a larger tissue sample 92 and maythus display individual cell or sub-cellular structures within thetissue sample 92. The cell maps or tissue images 104 may thereforecorrespond to one or more standardized fields-of-view selected based ona given protocol or operation, such as to achieve a desired spatialrepresentation, or may correspond to one or more user-selected orspecified fields-of-view. The cell map 104 may be created by selectionand execution of a suitable analysis algorithm, such as may beimplemented using selection box 108 and execution button 110. Forexample, in the depicted screen the analysis algorithm “Create Cell Map”has been selected at box 108 and executed to create cell map 104representing a selected field-of-view 94. In certain embodiments, theinterface may provide options (such as via a popup menu) allowing a userto configure the cell map 104, such as to add or clear a region ofinterest from the view, to select cells within the cell map 104 based onone or more of biomarker, cell type, DNA and/or RNA sequence orexpression, user applied highlighting, and so forth.

The pathway map 102 may be obtained and loaded from a variety of onlineor proprietary data sources and may be loaded from local files orimported from external data sources. In the depicted example, a pathwaymap 102 may be added, such as via a control interface 112, from aselectable list and registered via the interface. Once added, thepathway map 102 may be displayed graphically as a network of nodes andedges. In certain embodiments, the interface may provide options (suchas via a popup menu) allowing a user to configure the pathway map, suchas to add or clear a pathway map from the view or to set a state for anode or link within the pathway map 102, such as to set the state of apathway node to average, high, low, or undefined. By way of example, inone implementation a user may set a state of a selected node based on athree-state model, e.g., <x is low, x-to-y is medium, and >y is high. Inview of the various selection and configuration options provided to theuser, cells may be highlighted in the cell map 104 based on a pathwaymap state specified by the user, such as by specifying a state for oneor more nodes of the pathway map 102. Conversely, the state of one ormore nodes of the pathway map 102 may be set based upon the userselection of one or more cells within the cell map 104. That is, thelinkage between the cell map 104 and pathway map 102 allows a user tomake changes or selection in either map that results in changes made tothe state or display of the other map.

In certain implementations, the pathway maps 102 undergo an automatedpathway map registration process, which maps the pathway nodes and edgesto standard accession numbers (e.g., NCBI) of proteins, RNA, and genes.Performing such a registration process on the pathway nodes mayfacilitate algorithm implemented analysis across disparate data types,as discussed herein.

With respect to the pathway map(s) 102, in certain implementations oneor more visual indicators (e.g., colors and/or symbols) may be displayedin conjunction with the nodes of the pathway map 102. As used herein, anode 120 of a pathway map 102 should be understood to convey a varietyof possible information. For example, in certain implementations arespective node 120 can represent or convey a specific molecule, aspecific molecular state of such a molecule (e.g., whether the moleculeis phosphorylated, bound, and so forth), and/or a spatial location(e.g., extracellular or sub-cellular compartment locations (such as thenucleus, cytosol, plasma membrane, and so forth)). As used herein, andas discussed in greater detail below, a node 120 can link to protein IFmeasures (such as may be conveyed in the tissue images or maps) specificto the same relative spatial locations.

With respect to the use of visual indicators with the nodes 120, andturning to FIG. 5, two sample nodes 120 (e.g., EGFR and HER2) which maybe part of a pathway map 102 are depicted with various examples ofindicators that may be used to convey or to specify information about anode 120 in an implementation. By way of example, the displayed orindicated information may correspond to biomarker expression (e.g.,derived for cells or sub-cellular structures, individually or inaggregate, within a given field-of-view 94) and/or nucleic acid (e.g.,RNA, DNA, and so forth) sequence data (e.g., derived for a givensequencing region 96) for a subject for which a tissue cell map isconcurrently displayed. In the depicted example, indicators are shownwhich convey an inferred gene copy number (indicator 122 andaccompanying legend), DNA sequencing variant impact (indicator 124 andaccompanying legend), RNA expression measures (indicator 126 andaccompanying legend), and multiplexed immunofluorescence proteinmeasures (for HER2) (indicator 128 and accompanying legend).

In the depicted example, the subject has an inferred HER2 gene copynumber of 5.6 from the DNA sequencing data so a red hexagon indicator122 is displayed in the lower right hand corner of the HER2 node. TheHER2 RNA expression is high indicated by a red vertical bar indicator126. The HER2 protein IF measure is also high represented by thehorizontal red bar indicator 128. The EGFR gene has DNA mutations asindicated by the appearance of the DNA strand symbol indicator 124 onthe right side of the EGFR node. The probability that these mutationsare pathogenic has been scored as low (e.g., displayed as a blue DNAstrand symbol indicator). The impact of DNA mutations may be computedfrom a multivariate logistic model that generates a value representingthe probability of a DNA mutation being pathogenic vs. nonpathogenic orusing other suitable models. In certain implementations, the details ofa node's DNA mutations may be invoked for display, such as viewed in atable, by selecting a given node.

With the preceding discussion in mind, various examples are provided ofthe use of a data integration and query tool in accordance with thepresent approach. For example, turning to FIG. 6 a sample screen 150 isdepicted of an implementation where a user has set or otherwisespecified the state of one or more pathway nodes 120 in the pathway map102 resulting in cells that exhibit the specified pathway state at thenodes 120 in question being highlighted (e.g., highlighted red) in thecell maps 104. Further, in the depicted example, cell maps 104A and 104Bcorresponding, respectively, to two different subjects are displayedconcurrent with the pathway map 102, allowing the reviewer to comparethe different subjects based on the specified criteria.

To further elaborate on the depicted example, the samples in questionare both MYY IHC-positive, as indicated in selected patient data fields152. Correspondingly, the pathway map 102 state has been set to for highMYC, shown by a colored or highlighted horizontal bar (e.g., indicator128) for the MYC node 154. Further, the pathway map nodes 120 for GLUT1,HER2, RPS6 have been set to high and the pathway map node 120 for TP53has been set to low, as shown by their respective indicator bars. Inthis manner, the state of the pathway 102 has been defined based on thesettings of these nodes. Once the state of the pathway 102 is defined,an algorithm (e.g., Pathway>Cells) may be executed and, as an output ofsuch an algorithm, cells in the tissue images (e.g., cells maps 104) maybe highlighted which meet the defined pathway state criteria (e.g.,where the measured values at the cells in question have values that meetthe criteria defined by the nodes for which values have been set by theuser). Thus, a user may, based on known pathways and on measured,subject specific expression and sequence data, highlight individualcells (or sub-cellular structures) within a tissue image that exhibitcharacteristics specified in a linked pathway map.

Turning to FIGS. 7-9, these figures depict a more complex exampleinvolving the use of the present tool. In this example, a specificsub-population of cells is identified that exhibit a pathway state in acancer sample from one individual and the identified pathway state isthen used to screen (e.g., highlight) cells in a tissue sample fromanother individual. In this example, it can also be seen that cells maybe highlighted in fields of view 94 located at different tissuelocations.

Turning to FIG. 7, in this example cell maps 104 for two differentsubjects (shown as 104A and 104B) are displayed concurrent with a linkedpathway map 102. All cells in cell maps 104 having high HER2 proteinexpression are identified in two patients by setting the HER2 node 160in the pathway map 102 to high, shown by a colored horizontal bar (e.g.,indicator 128). In this example, cells within the cell maps 104 havinghigh HER2 are highlighted (e.g., shown in red or another specifiedcolor).

Turning to FIG. 8, from among the highlighted cells, a reviewer mayselect a cell or set of cells, e.g., a set of highlighted cells from oneof the cell maps 104. In this example, the reviewer has selected thecells in the bottom cell map 104B that were highlighted as having highHER2 expression levels. In one implementation, the selected cells may inturn be highlighted a different color (e.g., yellow) to indicate theirselected status. In this example, in response to the selection of thecells in the cell map 104B, the pathway map 102 is updated to set thestate of one or more nodes 120 based on the selected cells. For example,nodes where biomarker expression and/or nucleic acid expression orsequence measures are noteworthy or aberrant may be automatically setbased on the measures observed in the selected cells, as shown byindicators 122, 124, 126, 128. In this example, selected cells from onecell map are used to update the pathway map 102, which in turn causesthe highlighting of the cells within the other cell map 104 (i.e., theupper cell map 104A, in this example corresponding to a tissue samplefrom another patient or at a different field of view within the samesample) to be updated based on the new node settings. In this manner,cells in a different patient, tissue sample, or field of view may bequeried and selected by selecting cells in a given cell map (or tissuesample), which sets the state of an intermediary pathway map.

Further, turning to FIGS. 9A and 9B, an example is provided of a toolimplementation that is configured to highlight cells in different fieldsof view taken from different spatial locations of the same tissuesample. For example, in sample screen 170 of FIG. 9A a slide view pane172 is depicted showing the layout of a slide 90 having a tissue sampleundergoing analysis, where different fields-of-view 94 spatiallydistributed throughout the tissue sample have been imaged. A blowup ofthe slide view 172 is shown in FIG. 9B. Based on the settings of one ormore nodes in the pathway 102, certain of the fields-of-view 94 may haveimaged cells corresponding to the current state of the pathway map 102and these cells may be highlighted. As a result, certain of the fieldsof view 94 may be highlighted or have highlighted cells, and thesefields-of-view 94 may be shown in screen 170 of FIG. 9A as cells maps104. Examples, of such highlighted fields-of-view 94 are shown inenlarged form at the bottom of FIG. 9B. In addition, as shown in FIG.9B, for fields-of-view 94 where numerous cells meeting the pathwayconditions are present, it may be desirable to identify thesefields-of-view 94 for acquiring a tissue sample (indicated by sequencingregions 96, such as a 2 mm diameter sample area) for nucleic acidsequencing or other cellular analysis operations.

As shown in FIG. 9B, and as discussed with respect to FIG. 3, a givensequencing region or sample 96 may not correspond precisely to thegeometric shape, spatial location, and/or size of a correspondingfield-of-view 94, though in other embodiments they may so correspond.Thus, it should be appreciated that, due to differences between thesize, shape, or spatial location of a sequencing region 96 and acorresponding field-of-view 94, the sequence or other nucleic acid datafor a given sequencing region 96 may be based on or encompass somenumber of cells outside the field-of-view 94 or for which interest islimited.

Further, sequencing or other nucleic acid information obtained for agiven sequencing region 96 may be representative of the region 96 takenas a whole (i.e., may be averaged or aggregated for the correspondingregion 96) and, thus, may not provide data at the cellular orsub-cellular level in the manner that biomarker type data may beavailable for a corresponding field-of-view 94. As will be appreciated,this distinction will depend on the sampling and sequencingmethodologies employed, and to the extent that sequence data may beobtained at the cellular or sub-cellular level, this distinction may notapply. For example, to the extent that the sampling technique allows forselecting individual cells or a limited number of cells (e.g., 5, 10,20, and so forth) within the field-of-view 94, the sequencing or othernucleic acid data derived for a given sampled region 96 may correspondclosely to or precisely with cells of interest within the correspondingcell maps 104.

Turning to FIG. 10, it should also be appreciated that the presentapproach and tools provide additional flexibility, such as being able tocompare pathway map data for different patients. For example, in theexample screen 180, an implementation is shown where a reviewer hasloaded two copies (102A, 102B) of the same pathway map for comparison ofdifferent cells or tissues within a patient (i.e., a different copy ofthe pathway map 102 for each selected set of cells or tissues) or forcomparison of different patients (i.e., a different copy of the pathwaymap 102 for each patient). In this manner, different cells or tissues,either from the same individual or different individual, can be comparedin the pathway context. As will be appreciated, while the presentexample is of two copies of the pathway map 102, in practice more copiesof the pathway map (and hence more comparisons) may be displayed andcompared, within the limits imposed by available computation power anddisplay space.

In such an implementation, a reviewer may select cells (e.g., cancer ortumor cells) within each cell map (e.g., 104A or 104B) and, based uponthe measured or acquired biomarker expression and/or nucleic acid data,the respective linked pathway map (e.g., 102A or 102B) may be updated bysetting nodes in the respective pathway map based on the measured celldata. The reviewer may then compare pathway maps to find distinctionsbetween the selected cells and/or patients.

Turning to FIG. 11, based on the comparison pathways, a reviewer mayview the details of a node in question (e.g., the inferred JAK3 node188) in a more detailed format, e.g., a table 182. In this example, forinstance, the table 182 shows the results of a Gene Copy Numberalgorithm 186 and that the computed copy number for the JAK3 gene forthe patient (i.e., patient 184) associated with pathway 102B was 2.5.From the table, a researcher can see that the p-value for the computedcopy number is 0.008, which could be considered statisticallysignificant.

In addition, based on a pathway map 102 that has been specified or set,such as by selection of a selected set of cells within a cell map 104, ascoring algorithm may be applied to generate a score for the pathway map102. In such an implementation, the scoring algorithm (e.g., PathwayAnalysis algorithm 200 of FIG. 12) that is run will score the selectedpathway map 102 based on one or more criteria. For example, in oneembodiment, scores may be computed for the map's end point nodes for oneor more of protein synthesis, cell cycle, apoptosis, and/or cancer.Scores may be computed by such an algorithm using DNA sequence data orother available subject or tissue measures linked to the evaluatedpathway map 102. Scores for each pathway endpoint node may be computedand displayed, such as in a table 204. As will be appreciated, suchpathway map endpoint scores obtained for multiple patient pathway mapsmay be used to stratify or otherwise characterize patients.

As will be appreciated, other types of analyses may be implemented aspart of such a tool. For example a Genome-Wide Association Study (GWAS)210 may instead be selected and run as an analysis algorithm. Such ananalysis will find associations of common genetic variants in differentsubjects with a specific phenotype or end point measure. The input tothe GWAS algorithm consists of a list of samples and their phenotypevalues and a list of DNA variants present in one or more of the samples,as may be obtained by use of an analysis tool using the approachesdiscussed herein. The GWAS algorithm processes each variant, computingits frequency of being observed or not in the different phenotypegroups. The algorithm then computes a Pearson's Chi Square teststatistic for each variant to evaluate how probable the observedfrequencies differ from the expected frequencies that would occur due torandom chance. Results of one such analysis are shown in FIG. 13, whichshows a Manhattan Plot 212 of the DNA sequencing variants by theirchromosome position (x-axis) vs their association p-value to theendpoint measure of FDG uptake (y-axis). The red dotted line near thetop of the plot is the y-value required for a data point to beconsidered statistically significant after accounting for multipletesting. The table 214 shows the variants associated with theFDG_SUV_MAX endpoint measure across all subject samples. The table listwas sorted by each variant's association p-value of significance.

Similarly, a gene set enrichment analysis (GSEA) may be one of theanalysis algorithms employed or provided in accordance with the presentapproach. Such an analysis may accept as inputs a list of genemeasurements made on multiple samples with each sample assigned to aspecific phenotype. The gene measures could be RNA or protein expressionmeasures, or the presence of DNA variants in the genes. The GSEAalgorithm may also be provided one or more gene sets that can come froma gene set database, which may provide pathways and/or gene ontologysets. The algorithm then outputs the gene sets sorted by a p-value oftheir statistical significance. By way of example, in an embodiment, theimplemented algorithm may compute a correlation to phenotype for eachgene measure in the list, sort the gene list by computed correlationcoefficients, compute enrichment scores for each gene set, and estimatea statistical significance level of each enrichment score adjusting formultiple testing.

By way of further example, a specific GSEA analysis using aspects of theabove-described approach is provided. In this example, a GSEA algorithmincorporated as part of an analysis tool provides a data driven methodfor selecting a limited set of molecules of interest, or probes for suchmolecules, for a multi-molecular multiplexing study in which theexpression and/or state of the molecules of interest are statisticallycorrelated with the endpoint measure under study. The application ofmultiplexing IF study involves the step of selecting a list of probes(e.g., antibody markers) to use when staining the tissue samples forspecific proteins (including proteins in a particular phosphorylation,binding, or activation state) or other molecules of interest (e.g., anucleic acid strand having a specified sequence, and so forth. Thisprocess is straightforward if the specific molecules (e.g., proteins,RNA, and so forth) are already known, as is typically found in theclinical diagnosis setting. However, if instead the multiplexing studyis being conducted in the discovery research setting, it may instead beof interest to use an unbiased, data driven method of selecting targetmolecules and their corresponding antibody probes. This may beparticularly true if the investigator has existing data on the subjectssuch as DNA sequencing and/or RNA expression measures in addition to theclinical endpoint measurements under study.

The problem in such a context is to pick a limited set of molecules ofinterest that give the greatest amount of scientific information at theminimal amount of cost. For example, antibody probes used to visualizesuch molecules have a cost associated with them and tissue samples tendto be limited and are expensive to gather or purchase. The applicationof a GSEA provides a method of prioritizing molecules of interest (e.g.a given protein, a given protein state, an intermediary amino acidstructure, and/or nucleic acid sequence) by their probability of beingrelevant and associated with the endpoint measure under study, thusproviding the means to select a limited set of probes that will providethe most scientific benefit while minimizing the study's cost.

Turning to FIG. 14, a data driven method to select molecules of interestand/or corresponding probes is illustrated, with examples components andsteps to select a limited set of molecules of interest for amultiplexing study being shown. In this example, an existing database220 of markers (e.g., probes) that have been validated for use in themultiplexing platform is accessed as an input. The other form of input222 comes from existing biological knowledge bases of pathway maps,protein interaction networks, and gene ontology annotations, and publicscientific literature. The marker database 220 and biological knowledgebases 222 are used to create a Marker-Gene Sets database 224. TheMarker-Gene Sets database 224 contains for each validated marker a setof genes that are biologically associated with the gene targeted by themarker. The Marker-Gene Sets database 224 can be created in advance ofany planned multiplexing studies and can be periodically updated as newvalidated markers become available and to reflect changes in thebiological knowledge bases.

When an investigator is interested in conducting a multiplex study theyoften have a number of subjects in which they have endpoint measures230. The endpoint measure 230 may come from imaging such as Positronemission tomography (PET), Computed Tomography (CT), or Magneticresonance imaging (MRI), from patient outcome to a given therapy (e.g.recurrence status, survival), or some other clinical measurement orsubject phenotype. For each subject, the investigator may have DNAsequencing data 232 and/or RNA gene expression (e.g., RNA microarray)measures 234 for one or more sequencing regions 96. This data incombination with the endpoint measures 230 (e.g., a selected endpointphenotype) for each subject are used to perform an analysis 240 (such asa Gene Set Enrichment Analysis (GSEA), by way of example) represented bysteps 242, 244, 246. This algorithm 240 can be used to compute thecorrelation of each gene measured by DNA sequencing or RNA geneexpression with the endpoint measure under study (block 242). The listof all genes measured is then sorted by the absolute value of theircorrelation coefficient (block 244). The final step of the GSEAalgorithm is to calculate (block 246) an enrichment score for each geneset and estimate its statistical significance level. The Marker-GeneSets database 224 is used as the gene sets to work with by the GSEAalgorithm at step 246. The list of Marker-Gene Sets is then sorted bytheir estimated significance level and is displayed (block 250) to theinvestigator. In one embodiment, the markers that are presented at thetop of the list are those that are both validated and approved for useand also are likely to be associated with the endpoint measure understudy.

While certain examples of analysis algorithms are noted in detail above,it should be appreciated that a variety of analysis algorithms andalgorithm options that leverage both the pathway and cell image maps maybe provided. Certain examples of such algorithms and options include,but are not limited to: options to highlight (or otherwise visuallymark) pathway nodes 120 if they are a target for a validated antibody orare otherwise a measureable node; options to plot DNA sequencingmutations for a selected sample region 96 to a current pathway map 102;options to plot DNA FISH measures for selected cells in a current cellmap 104 to a current pathway map 102; options to plot RNA expressionmeasures for the selected sample region 96 to a current pathway map 102;options to plot IF protein measures for the selected cells in a currentcell map 104 to a current pathway map 102; options to plot all availablemeasures for the selected cells in a current cell map 104 to a currentpathway map 102; options to visually highlight cells in a current cellmap 104 using a current pathway map state; options to select cells in acurrent cell map 104 based on cell type; options to select cells in acurrent cell map 104 bounded by one or more defined regions-of-interest;options to select cells in a current cell map 104 bounded by one or moreDNA sequencing regions-of-interest; options to select cells based on abiomarker(s) IF measurement(s); options to find the shortest path (e.g.,edge connection) between two selected nodes 120 in a pathway map 102;options to display the gene copy number for a user-inputted gene symbol;and options to create threshold for a study and/or for each slide withina study using available field-of-view single cell analysis (SCA) data(e.g., thresholds may be created for one or more of 2, 3, 4, or 5 statemodels). Where appropriate, for one or more of the presented options auser may specify threshold values (e.g., low, medium, high, average,median, mode, and so forth based on a given statistical distribution orapproach) to be met for implementations of the respective option.

With the preceding discussion and examples in mind, it should beappreciated that the present approaches and related tools may be usefulin a generalized sense for aggregating and analyzing molecular data andbiochemical or regulatory pathways in a variety of different contexts.For example, using one or more of the features and operations describedabove, users may be able to perform an analysis or study that leveragesboth sequence and image data to generate hybrid images that may beuseful in clinical, diagnostic or research contexts.

By way of example, and turning to FIG. 15, a high-level view of onepotential study protocol is shown that may employ certain of thetechniques discussed herein. In this example, a tissue sample 92 isacquired from a subject and some subset of cells (e.g., a tumor, lesion,or other abnormality) of the sample 92 are sequenced 280 to derivenucleic acid sequence information 282 (e.g., mutation sequence data) forthe cells in question. In one embodiment, the sequencing 280 isperformed on cells in a heterogeneous or other non-specific context sothat the sequence information 282 is not tied to a spatial contextpresent in images of the tissue sample 92. Conversely, in otherembodiments the sequencing 280 is performed on a generally homogeneoussample of cells derived from a localized region (e.g., a tumor, lesion,or other abnormality) within the tissue sample 92. Based on the sequencedate 282, a GSEA analysis 286 (as described herein) or other sequenceanalysis may be conducted and a suitable set of IF probes 290 (e.g.,labeled or tagged antibodies) selected from a larger catalog ofavailable probes 292. The tissue sample 92 (e.g., slides formed from thetissue sample) may then undergo multiplexed IF imaging using theselected antibodies 290 to generate multiplexed IF images 296 whichdepict the spatial locations of the selected mutations within the tissuesample 92. Based on these images, a user may then identify, extract,view, and/or analyze regions of interest 298 (e.g., specific fields ofview) within the multiplexed IF tissue sample images 296. Thus, in thisexample, sequence or mutation information 282 for a tissue sample 92 maybe used to select markers (e.g., probes) 290, which may then be used ina multiplexed imaging approach to visualize cells of interest within asample based on the initial sequence analysis. It should also beappreciated that certain of these steps and actions may be iterativelyperformed. By way of example, once one or more regions of interest 298are identified in the multiplexed tissue sample image 296, cell samplesmay be extracted from these regions-of-interest within the tissue samplefor further sequencing and analysis, which may lead to the selection ofadditional probes for use in additional imaging rounds.

Conversely, the tools and techniques discussed herein may be used tofacilitate other analyses or data acquisitions, such as to acquire amutational profile for spatially-selected regions. For example, turningto FIG. 16 a further high-level view is depicted of a different studyprotocol employing techniques and tools discussed herein to acquirespatially-selected DNA sequence data. In this example, a tissue sample92 undergoes multiplexed IF imaging using probes 290 selected from alibrary of probes 292 and corresponding to molecules determined to be ofinterest, resulting in one or more multiplexed IF images 296immunofluorescently tagged for biomarker expression deemed of interest.From within the multiplexed IF images 296, regions-of-interest 298 maybe identified or extracted that spatially localize expression activityof interest (e.g., protein, nucleic acid, or other biologicalexpression) within the tissue sample 92. Cells samples may then be taken(e.g., at one or more sampling or sequencing regions 96) that correspondto the identified spatial locations within the tissue sample 92 andsequencing 304 may be performed on the spatially selected cells togenerate a mutational profile 306 that is generally specific to thecells within the identified spatial regions-of-interest 298. It shouldalso be appreciated that certain of these steps and actions may beiteratively performed. By way of example, once sequence data has beenobtained for cells in the one or more regions of interest 298,additional probes may be identified for newly identified molecules ofinterest, and the tissue sample 92 reimaged using the newly selectedprobes. In this manner, additional regions of interest can be identifiedand subsequently sequenced. Such an approach may be of particularinterest in fields such as oncology where identification of localizedmutations and aberrant expression events is of particular interest.

Technical effects of the invention include the dynamic linking ofdisplayed pathway maps and cell maps, where the pathway maps are linkedto spatially-localized regional nucleic acid data (e.g., sequence data),as opposed to non-spatially selected nucleic acid data. The pathway mapand cell map data is linked so that interactions (e.g., selections ofcells, setting of node values or states, and so forth) results inchanges or updates to the linked map, such as the selection orhighlighting of cells exhibiting pathway map characteristics specifiedby a user or updating node values or states to correspond to that of acell or cells selected by the user.

This written description uses examples to disclose the invention,including the best mode, and also to enable any person skilled in theart to practice the invention, including making and using any devices orsystems and performing any incorporated methods. The patentable scope ofthe invention is defined by the claims, and may include other examplesthat occur to those skilled in the art. Such other examples are intendedto be within the scope of the claims if they have structural elementsthat do not differ from the literal language of the claims, or if theyinclude equivalent structural elements with insubstantial differencesfrom the literal languages of the claims.

The invention claimed is:
 1. A computer-based method for interactivelyevaluating image and data for a tissue sample, comprising: displaying apathway map comprising a plurality of nodes linked to nucleic acidsequence data for one or more spatially localized regions-of-interestwithin a tissue sample; displaying a cell map depicting a set of cellspresent within a field-of-view of the tissue sample, wherein the cellmap is linked to a plurality of biomarker expression data displayed forthe tissue sample; receiving one or more inputs specifying values orstates for one or more nodes of the pathway map; and based on the one ormore inputs, highlighting cells within the cell map that exhibitbiomarker expression corresponding to the values or states specified forthe one or more nodes.
 2. The computer-based method of claim 1, whereinthe regions-of-interest for which nucleic acid sequence data is knowndiffer in one or both of size or shape from the fields-of-viewassociated with the cell map.
 3. The computer-based method of claim 1,wherein the nucleic acid sequence data is averaged or aggregated for arespective region-of interest.
 4. The computer-based method of claim 1,wherein the biomarker expression data is at the cellular or sub-cellularlevel for cells within the cell map.
 5. The computer-based method ofclaim 1, wherein the biomarker expression corresponds to a mutationprofile characterized by the values specified for the one or more nodesby the inputs.
 6. The computer-based method of claim 1, wherein thepathway map and the cell map are displayed concurrently and whereinreceipt of the one or more inputs, or changes to the inputs, dynamicallyupdates the highlighting of cells.
 7. The computer-based method of claim1, wherein the pathway map comprises a metabolic pathway map orsignaling pathway map.
 8. The computer-based method of claim 1, whereinthe one or more inputs specifying values or states for one or more nodesof the pathway map comprises user selections of a cell or subset ofcells in the cell map.
 9. The computer-based method of claim 1, whereinone or more of the nodes are displayed with visual indicators conveyinginformation about biomarker expression or nucleic acid sequence for therespective node.
 10. The computer-based method of claim 9, wherein theconveyed information comprises one or more of biomarker expression,inferred gene copy number, DNA sequencing variant impact, RNAexpression, or immunofluorescence protein measures.
 11. Thecomputer-based method of claim 1, wherein the one or more inputs specifya value or state related to a gene copy number, DNA sequence variantimpact, RNA expression measure, or immunofluorescence protein expressionmeasure.
 12. A computer-based method for interactively evaluating imageand data for a tissue sample, comprising: displaying a pathway mapcomprising a plurality of nodes linked to nucleic acid sequence data forone or more spatially localized regions-of-interest within a tissuesample; displaying a cell map depicting a set of cells present within afield-of-view of the tissue sample, wherein cell map is linked to aplurality of biomarker expression data for the tissue sample; receivingone or more inputs selecting one or more cells of the cell map; andbased on the one or more inputs, setting values or states of one or morenodes within the pathway map to correspond to the nucleic acidcharacteristics of the one or more selected cells.
 13. Thecomputer-based method of claim 12, wherein the nucleic acid sequencedata is averaged or aggregated for a respective region-of interest. 14.The computer-based method of claim 12, wherein the biomarker expressiondata is at the cellular or sub-cellular level for cells within the cellmap.
 15. The computer-based method of claim 12, wherein the nucleic acidcharacteristics of the one or more selected cells correspond to amutation profile for the one or more selected cells.
 16. Thecomputer-based method of claim 12, wherein the pathway map and the cellmap are displayed concurrently and wherein receipt of the one or moreinputs, or changes to the inputs, dynamically updates the highlightingof cells.
 17. The computer-based method of claim 12, wherein the one ormore inputs selecting one or more cells of the cell map select cellsexhibiting biomarker expression for one or more biomarkers associatedwith a mutation profile.
 18. A processor-based system, comprising: oneor both of a memory or storage device storing one or more executableroutines for the analysis of region-specific nucleic acid sequence dataand cellular or sub-cellular biomarker expression data; one or moreprocessors configured to execute the one or more executable routineswhich, when executed, cause acts to be performed comprising: displayinga pathway map comprising a plurality of nodes linked to nucleic acidsequence data for one or more spatially localized regions-of-interestwithin a tissue sample; displaying a cell map depicting a set of cellspresent within a field-of-view of the tissue sample, wherein the cellmap is linked to a plurality of biomarker expression data for the tissuesample; receiving inputs setting one or more node values or stateswithin the pathway map or selecting one or more cells within the cellmap; and if the inputs set one or more node values or states within thepathway map, highlighting cells within the cell map that exhibitbiomarker expression corresponding to the values or states specified forthe one or more nodes; or if the inputs select one or more cells withinthe cell map, setting values of one or more nodes within the pathway mapto correspond to the nucleic acid characteristics of the one or moreselected cells.
 19. The processor-based system of claim 18, wherein theregions-of-interest for which nucleic acid sequence data is known differin one or both of size or shape from the fields-of-view associated withthe cell map.
 20. The processor-based system of claim 18, wherein thenucleic acid sequence data is averaged or aggregated for a respectiveregion-of interest.
 21. The processor-based system of claim 18, whereinthe biomarker expression data is at the cellular or sub-cellular levelfor cells within the cell map.
 22. The processor-based system of claim18, wherein the pathway map and the cell map are displayed concurrentlyand wherein receipt of the one or more inputs, or changes to the inputs,dynamically updates the highlighting of cells.